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Exporting to a BioPAX File

asked 2018-06-01 13:19:05 -0500

JW Carlson gravatar image

I've been using BioPAX files to export pathologic results. I've noticed two issues recently:

1) With my older version of pathway-tools (v20.0), it looks like superpathways are not exported in the level 3 owl file, but appear to be there in the level 2 file. The specific one I was looking at is carotenoid biosynthesis in MetaCyc.

2) Since I realize that I'm using an old version, I downloaded and installed v22.0. Here is notice that I cannot export a DB to a BioPAX file - the option is greyed out. Is this operation no longer possible? I've tried v20.5 and v22.0 on linux and could not export a BioPAX file but can in v20.0.


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answered 2018-06-04 18:54:15 -0500

JW Carlson gravatar image

Thanks for the response. I apparently had jumped to a conclusion from the fact that CAROTENOID-PWY was missing and assumed it was a problem that superpathways that were missing.

What I'm really doing here is running pathologic on a set of proteomes and seeing that there are pathways in the pathologic runs that are not in the MetaCyc knowledgebase. There were 38 missing pathways altogether in 1 organism run; the first few I checked were superpathways and I extrapolated from there. Does it make sense to you that there would be a data problem that would prevent a pathway getting exported from MetaCyc that would not prevent a pathway getting exported from a pathologic analysis?

Another thing I have noticed is that there are occasionally slight difference between the pathway topology in the output files generated in runs with different organisms by pathologic. Does this also make sense?

I am going to try to do the head-to-head comparison using v22.

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Sorry! I just realized I lied. I see CAROTENOID-PWY in my organism run when I export data using lisp functions that call (all-pathways). I do not see this pathway as port of the .owl file from my pathologic run.

JW Carlson gravatar imageJW Carlson ( 2018-06-04 19:11:20 -0500 )edit

Nothing about whether a pathway can be exported to biopax would effect whether or not it could be predicted by pathologic -- the criteria are completely different. Pathologic cannot predict any pathway that is not in MetaCyc, regardless of whether it is in the biopax export file. I'm not sure what you mean by different topologies, or which output files you're referring to -- are we still talking about biopax output files? I'm not sure why topologies would be different, assuming all were built from the same version of metacyc, though I think for a superpathway it's possible that if one of the sub-pathways is missing from one organism, the topology of the superpathway will reflect that. If you're talking about our generated pathway diagrams, I could believe that they might look slightly different in different organisms.

Suzanne Paley gravatar imageSuzanne Paley ( 2018-06-04 20:49:28 -0500 )edit

I have an example of a simple (what's the opposite of super?) pathway that is different in 2 organisms after a run of pathologic. PWY-6887 (kauralexin biosynthesis). In one organism, I see geranylgeranyl diphosphate -> (-)-ent-copalyl diphosphate and then branch to either ent-kaurene or ent-isokaurene. In another organism, (-)-ent-copalyl diphosphate produces only ent-isokaurene. ent-kaurene exists on a disconnected branch. In the first organism I have proteins assigned to the enzymes associated with (-)-ent-copalyl diphosphate -> ent-kaurene and the second I do not. Is that why the diagram is disconnected. (Is there some way for me to post screenshot of the diagrams?)

JW Carlson gravatar imageJW Carlson ( 2018-06-07 13:41:02 -0500 )edit

PWY-6887 is actually a super-pathway, since it contains the ent-kaurine biosynthesis pathway. If that sub-pathway is not predicted, then all you'll see of the superpathway is all the reactions except for the two from geranylgeranyl diphosphate to ent-kaurene (which disconnects the pathway).

Suzanne Paley gravatar imageSuzanne Paley ( 2018-06-09 18:42:37 -0500 )edit

answered 2018-06-01 23:05:47 -0500

Suzanne Paley gravatar image

This is not a problem with superpathways in general. It seems to be a problem with this particular pathway. If there is any component of a pathway that causes trouble for our biopax exporter (due to a representation mismatch of some kind) then the whole pathway cannot be exported. Because biopax2 and biopax3 are so different, entities that have problems for one may still work for the other, which is why that pathway still appears in the biopax2 file.

That said, the issue that is causing a problem in this case is nothing fundamental, and probably amounts to a data error on our end (though not one that causes problems in any other context). I have asked our MetaCyc curator to look into it, so hopefully it can be fixed for the next release (and we can probably output that pathway to biopax as soon as the problem is fixed and send it to you directly, if you need it sooner than the next release).

As to the menu command, it is enabled for any pgdbs that are not part of your distribution (i.e. any that you download from the registry or create yourself), but EcoCyc and MetaCyc are built-in, and since we provide the biopax files with the distribution, and the pgdbs cannot be modified, there is no reason to ever invoke that command on EcoCyc or MetaCyc. Therefore, we have disabled it.

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We have fixed the problem with this pathway, so biopax3 output for it should now be included in our next release.

Suzanne Paley gravatar imageSuzanne Paley ( 2018-06-12 12:08:19 -0500 )edit

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Asked: 2018-06-01 13:19:05 -0500

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Last updated: Jun 04 '18